Running PDBSTAT from Linux Ayuda is on: /farm/software/PdbStat/PdbStat-5.9 (C) (C) Pdbstat -- A program to evaluate some statistics of macromolecules, (C) given the cartesian coordinates. (C) (C) (c) Copyright 1992-2013 Roberto Tejero and Gaetano T. Montelione (C) Center for Advanced Technology and Medicine (CABM) (C) Rutgers University (C) ** VERSION: 5.9-exp mar may 14 00:20:00 UTC 2013 ** ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ===============> W E L C O M E to PDBStat <================ PDBStat has become a tool able (between other things) of: a) read and interconvert between DISMAN, DYANA, PDB, DISCOVER, IMPACT b) elaborate some info about the molecule as MW, Radius of gyration, .. c) investigate the setereochemical quality of a protein by evaluating phi, psi, chi1, impropers and chirality The sequence of acts should be: 1.- read a file (coords, constr) 2.- read a sequence file (can be free format) 3.- Follow menu (calculating, writing ...) HAVE FUN AND ENJOY !! **** For more info type `help' or `menu' **** --> ... Reading/Loading Distances file ... 125 distance records read --> ... Reading/Loading Dihedral Library .. 1119 library records read PdbStat> [rea]d [hel]p [his]tory [men]u [phi] [qui]t... PdbStat> leyendo PDB > locate_file(): file `DHR8C_R3Cons_em_bcr3.pdb' opened for reading > ReadCoordsPdb(): >> EXPDTA NMR, 21 STRUCTURES > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> REMARK PdbStat -- PDB COORDINATES FOR TEMP_BCM_111.PDB, 20 MODEL/S TEMP_BCM_111.PDB > ReadCoordsPdb(): >> REMARK PdbStat -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ReadCoordsPdb(): >> SEQRES 1 A 71 MET ASP ASN ARG GLN PHE LEU SER LEU THR GLY VAL SER > ReadCoordsPdb(): Counting models in file `DHR8C_R3Cons_em_bcr3.pdb'; Model: > ReadCoordsPdb(): After scanning there is(are) 20 model(s) > ReadCoordsPdb(): what model do you want [(1 to 20) or all] ?_ > ReadCoordsPdb(): Reading *all* models in file DHR8C_R3Cons_em_bcr3.pdb > ReadCoordsPdb(): Reading a total of (20) models in file > ReadCoordsPdb(): I'm reading!, model 0 > ReadCoordsPdb(): *** SUMMARY *** > ReadCoordsPdb(): --> 45520 ATOM records read from file > ReadCoordsPdb(): --> 45520 Regular IUPAC Atoms > ReadCoordsPdb(): --> 0 Pseudo-atoms (DISMAN type) > ReadCoordsPdb(): --> 0 Lone pairs > ReadCoordsPdb(): Bye ... > ReadCoordsPdb(): ** monomer, 1 [1] chains ** PdbStat> > calc_order_parameters(): ... Evaluating Dihedrals CHAIN .GT. SUM.GT. RES ID DIH S(phi) S(psi) S(chi1) S(chi2) S(chi3) S(chi4) S(chi5) 0.90 1.6 ----------------------------------------------------------------------------------- MET M 1 0.146 0.632 0.355 0.311 ASP M 2 0.551 0.376 0.498 0.909 ASN M 3 0.570 0.676 0.663 0.622 ARG M 4 0.742 0.943 0.910 0.930 0.544 0.839 1.000 GLN M 5 0.986 0.997 0.920 0.995 0.897 5 5 PHE M 6 0.998 0.995 0.913 0.563 6 6 LEU M 7 0.995 0.999 0.998 1.000 7 7 SER M 8 0.999 0.999 0.998 8 8 LEU M 9 0.997 0.999 0.996 0.999 9 9 THR M 10 0.989 0.945 0.439 10 10 GLY M 11 0.950 0.994 11 11 VAL M 12 0.997 0.998 1.000 12 12 SER M 13 0.996 0.994 0.634 13 13 LYS M 14 0.999 0.995 0.795 1.000 0.999 1.000 14 14 VAL M 15 0.999 0.999 1.000 15 15 GLN M 16 0.999 1.000 1.000 0.809 0.907 16 16 SER M 17 0.999 0.999 1.000 17 17 PHE M 18 0.992 0.996 0.996 0.990 18 18 ASP M 19 0.996 0.999 0.999 0.998 19 19 PRO M 20 0.996 0.998 0.945 0.887 20 20 LYS M 21 0.998 0.997 0.999 0.999 0.999 0.999 21 21 GLU M 22 0.999 0.999 1.000 0.999 0.961 22 22 ILE M 23 0.997 0.999 0.999 0.769 23 23 LEU M 24 0.999 0.997 0.999 0.999 24 24 LEU M 25 0.998 0.997 0.999 1.000 25 25 GLU M 26 0.998 0.999 0.999 0.997 0.912 26 26 THR M 27 0.992 0.978 0.538 27 27 ILE M 28 0.864 0.130 0.998 0.848 GLN M 29 0.108 0.966 0.843 0.583 0.731 GLY M 30 0.897 0.985 30 VAL M 31 0.986 0.996 1.000 31 31 LEU M 32 0.996 0.998 0.997 0.999 32 32 SER M 33 0.999 0.999 0.917 33 33 ILE M 34 0.999 1.000 1.000 0.999 34 34 LYS M 35 0.999 0.999 1.000 0.932 0.934 0.872 35 35 GLY M 36 0.998 0.998 36 36 GLU M 37 0.995 1.000 0.443 1.000 1.000 37 37 LYS M 38 0.999 0.999 1.000 0.852 1.000 1.000 38 38 LEU M 39 1.000 0.989 0.999 0.998 39 39 GLY M 40 0.945 0.914 40 40 ILE M 41 0.616 0.461 0.580 0.691 LYS M 42 0.462 0.271 0.566 0.936 0.931 0.998 HIS M 43 0.571 0.550 0.473 0.434 LEU M 44 0.754 0.242 0.587 0.577 ASP M 45 0.625 0.288 0.553 0.906 LEU M 46 0.325 0.494 0.525 0.567 LYS M 47 0.445 0.847 0.566 0.998 1.000 0.999 ALA M 48 0.791 0.751 GLY M 49 0.736 0.946 GLN M 50 0.975 0.998 0.523 0.998 0.714 50 50 VAL M 51 0.999 0.998 0.865 51 51 GLU M 52 0.998 0.996 0.673 0.998 0.903 52 52 VAL M 53 0.999 0.991 0.415 53 53 GLU M 54 0.993 0.996 0.275 0.997 0.843 54 54 GLY M 55 0.995 0.993 55 55 LEU M 56 0.993 0.992 0.998 0.940 56 56 ILE M 57 0.999 0.994 0.731 1.000 57 57 ASP M 58 0.993 0.992 0.995 0.935 58 58 ALA M 59 0.995 0.998 59 59 LEU M 60 0.993 0.995 0.996 0.997 60 60 VAL M 61 1.000 0.997 1.000 61 61 TYR M 62 0.993 0.978 0.843 0.654 62 62 PRO M 63 0.993 0.779 0.947 0.912 LEU M 64 0.741 0.325 0.449 0.624 GLU M 65 0.280 0.108 0.564 0.855 0.940 HIS M 66 0.406 0.354 0.591 0.407 HIS M 67 0.753 0.488 0.457 0.676 HIS M 68 0.457 0.140 0.599 0.711 HIS M 69 0.640 0.199 0.361 0.708 HIS M 70 0.345 0.494 0.321 0.349 HIS M 71 0.824 0.287 0.653 0.622 MET M 82 0.240 0.147 0.632 0.356 0.312 ASP M 83 0.551 0.376 0.498 0.909 ASN M 84 0.570 0.676 0.663 0.622 ARG M 85 0.742 0.943 0.910 0.930 0.544 0.839 1.000 GLN M 86 0.986 0.997 0.920 0.995 0.897 86 86 PHE M 87 0.998 0.995 0.913 0.563 87 87 LEU M 88 0.995 0.999 0.998 1.000 88 88 SER M 89 0.999 0.999 0.998 89 89 LEU M 90 0.997 0.999 0.996 0.999 90 90 THR M 91 0.989 0.945 0.439 91 91 GLY M 92 0.950 0.994 92 92 VAL M 93 0.997 0.998 1.000 93 93 SER M 94 0.996 0.994 0.634 94 94 LYS M 95 0.999 0.995 0.795 1.000 0.999 1.000 95 95 VAL M 96 0.999 0.999 1.000 96 96 GLN M 97 0.999 1.000 1.000 0.809 0.907 97 97 SER M 98 0.999 0.999 1.000 98 98 PHE M 99 0.992 0.996 0.995 0.990 99 99 ASP M 100 0.996 0.999 0.999 0.998 100 100 PRO M 101 0.996 0.998 0.945 0.887 101 101 LYS M 102 0.998 0.997 0.999 0.999 0.999 0.999 102 102 GLU M 103 0.999 0.999 1.000 0.999 0.961 103 103 ILE M 104 0.997 0.999 0.999 0.769 104 104 LEU M 105 0.999 0.997 0.999 0.999 105 105 LEU M 106 0.998 0.997 0.999 1.000 106 106 GLU M 107 0.998 0.999 0.999 0.997 0.912 107 107 THR M 108 0.992 0.977 0.538 108 108 ILE M 109 0.864 0.130 0.998 0.848 GLN M 110 0.108 0.966 0.844 0.584 0.732 GLY M 111 0.897 0.985 111 VAL M 112 0.986 0.996 1.000 112 112 LEU M 113 0.996 0.998 0.997 0.999 113 113 SER M 114 0.999 0.999 0.917 114 114 ILE M 115 0.999 1.000 1.000 0.999 115 115 LYS M 116 0.999 0.999 1.000 0.932 0.934 0.872 116 116 GLY M 117 0.998 0.998 117 117 GLU M 118 0.995 1.000 0.443 1.000 1.000 118 118 LYS M 119 0.999 0.999 1.000 0.852 1.000 1.000 119 119 LEU M 120 1.000 0.989 0.999 0.998 120 120 GLY M 121 0.945 0.914 121 121 ILE M 122 0.615 0.461 0.580 0.692 LYS M 123 0.462 0.271 0.566 0.936 0.931 0.998 HIS M 124 0.571 0.550 0.474 0.434 LEU M 125 0.754 0.242 0.587 0.576 ASP M 126 0.625 0.288 0.553 0.906 LEU M 127 0.326 0.494 0.525 0.567 LYS M 128 0.445 0.847 0.566 0.998 1.000 0.999 ALA M 129 0.791 0.751 GLY M 130 0.736 0.946 GLN M 131 0.975 0.998 0.523 0.998 0.714 131 131 VAL M 132 0.999 0.998 0.865 132 132 GLU M 133 0.998 0.996 0.673 0.998 0.903 133 133 VAL M 134 0.999 0.991 0.415 134 134 GLU M 135 0.993 0.996 0.275 0.997 0.843 135 135 GLY M 136 0.995 0.993 136 136 LEU M 137 0.993 0.992 0.998 0.940 137 137 ILE M 138 0.999 0.994 0.731 1.000 138 138 ASP M 139 0.993 0.992 0.995 0.935 139 139 ALA M 140 0.995 0.998 140 140 LEU M 141 0.993 0.995 0.996 0.997 141 141 VAL M 142 1.000 0.997 1.000 142 142 TYR M 143 0.993 0.978 0.843 0.653 143 143 PRO M 144 0.993 0.778 0.947 0.912 LEU M 145 0.741 0.324 0.449 0.623 GLU M 146 0.280 0.108 0.564 0.855 0.940 HIS M 147 0.406 0.353 0.591 0.407 HIS M 148 0.753 0.488 0.457 0.676 HIS M 149 0.457 0.140 0.599 0.711 HIS M 150 0.640 0.199 0.361 0.708 HIS M 151 0.345 0.494 0.321 0.349 HIS M 152 0.824 0.653 0.622 Ranges: 6 from: M 5 to M 27 from: M 31 to M 40 from: M 50 to M 62 from: M 86 to M 108 from: M 112 to M 121 from: M 131 to M 143 PdbStat> > do_average_coords(): Making average for backbone atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for backbone onto model 1 > do_average_coords(): Calc. average coordinates backbone > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 1 is: 0.469 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 2 is: 0.695 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 3 is: 0.351 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 4 is: 0.423 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 5 is: 0.360 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 6 is: 0.359 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 7 is: 0.462 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 8 is: 0.449 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 9 is: 0.375 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 10 is: 0.599 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 11 is: 0.400 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 12 is: 0.554 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 13 is: 0.243 (*) > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 14 is: 0.438 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 15 is: 0.530 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 16 is: 0.352 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 17 is: 0.302 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 18 is: 0.365 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 19 is: 0.347 > Kabsch RMSD of backbone atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 20 is: 0.328 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..27],[31..40],[50..62],[86..108],[112..121],[131..143], is: 0.420 > Range of RMSD values to reference struct. is 0.243 to 0.695 > do_average_coords(): Making average for heavy atoms > do_average_coords(): Calculating center of masses > do_average_coords(): Calling optimal rotation for heavy onto model 1 > do_average_coords(): Calc. average coordinates heavy > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 1 is: 0.733 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 2 is: 1.212 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 3 is: 0.618 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 4 is: 0.719 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 5 is: 0.627 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 6 is: 0.558 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 7 is: 0.667 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 8 is: 0.706 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 9 is: 0.593 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 10 is: 1.021 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 11 is: 0.596 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 12 is: 0.693 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 13 is: 0.591 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 14 is: 0.684 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 15 is: 0.860 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 16 is: 0.834 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 17 is: 0.518 (*) > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 18 is: 0.607 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 19 is: 0.537 > Kabsch RMSD of heavy atoms in res. M[5..27],M[31..40],M[50..62],M[86..108],M[112..121],M[131..143],for model 20 is: 0.620 > > Kabsch RMSD statistics for 20 structures: > Mean RMSD using as refer. str. `average' for res.[5..27],[31..40],[50..62],[86..108],[112..121],[131..143], is: 0.700 > Range of RMSD values to reference struct. is 0.518 to 1.212 PdbStat> PdbStat> *END* of program detected, BYE! ...